Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-01-30

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15:38 blackrim towodo: we don't have a draft 17 of taxonomy yet do we? just making sure that folks aren't waiting for me to load that before making comments
15:40 towodo you can have one if you like but it's not clear to me what's happening either.  looks like draft 16 got very little review. i've fixed all the problems that were submitted, i think, but will need to check
15:41 towodo i mean, come on, only about 10 complaints?  there are thousands, if not tens of thousands, of problem spots
15:41 blackrim josephwb has some more edits that he is working on but maybe he is using the patch file
15:42 towodo i was sort of waiting to hear about reptilia. i think i fixed pongidae
15:43 blackrim i will poke plants and chris/keith again to see if that was it -- i need to double check my plant files
15:44 towodo i've been poking around in insects. Formicidae is a godawful mess. have poked friends about alternative taxonomy source
15:44 towodo GBIF's ant classification dates from 1877
15:45 towodo will try doing a run now so i can check my edits
15:46 towodo nothing has been checked into the patch system
15:46 blackrim i don't know if peter can help with the insects some?
15:46 blackrim he suggested he could look at spiders
15:48 josephwb yeah, I will come up with some patch commands to fix reptilia
15:48 towodo there's a bunch of taxa directly under arachnida that could be put in better places e.g. mites… but that's unrewarding work
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16:51 PEM <towodo>Adding the fossil column to IF - what value (True,1,yes, etc.) will smasher be looking for?
16:51 towodo the column should be called 'flags' and the value should be either empty or 'extinct'
16:52 PEM <towodo>thanks
16:52 towodo does IF distinguish between fossil and extinct?  some orgs with fossils are not extinct
16:52 towodo or so i hear
16:53 PEM Not that I can tell - there are some groups that are named 'fossil xxx' and any child of those I'm assuming are extinct.
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17:16 towodo blackrim, I got tired of waiting so made a draft17 for you.
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17:29 blackrim ok, thanks, I will incorporate now
17:51 kcranstn stephen, will you be at next week's all hands call (while I am giving my phyloseminar?)
17:58 blackrim I should be. the only weird bit is i may have to leave a few minutes early (guest lecture for a class here right after)
18:00 kcranstn you logging onto skype now?
18:01 blackrim yep, getting there (it is on a computer i don't use much :-p)
18:01 towodo blackrim, a great example of 'tattered' or residual taxa is Artiodactyla, which shows up as sibling to Theria
18:02 towodo I am tempted to just mark it 'incertae sedis' and suppress it
18:02 towodo Erinaceomorpha is similar
18:03 blackrim ok, Artiodactyla is a good taxon in general so that is interesting
18:06 towodo in that case the question is: Would things be better if the remaining children of Art. became children of the MRCA of all the Art. children? and Art. proper suppressed?
18:06 blackrim yeah, that is one that it would be good to get Chris or Keith to answer (I think). i am not an animal person
18:07 kcranstn aren't we on skype right now ;)
18:07 blackrim we are there too :-)
18:17 kcranstn I sense that we need a deadline for the taxonomy edits
18:17 kcranstn and tree lists
18:20 blackrim yeah, I had a deadline as tomorrow for the tree lists (so seems like all of them will have it then if chris gets it)
18:21 kcranstn ok, good
18:21 blackrim towodo: just FYI my plant runs that check for some errors finished without major issues
18:30 towodo it looks like the seven residual Artiodactyla are all extinct, but not marked as such
18:31 blackrim interesting
18:31 blackrim something for Chris and Keith to talk about
18:38 blackrim ok, apparently I need to update my animal knowledge -- from wikipedia "Cetartiodactyla is the clade in which whales (including dolphins) and even-toed ungulates have currently been placed. The term was coined by merging the name for the two orders, Cetacea and Artiodactyla, into a single word. The term Cetartiodactyla reflects the idea that whales evolved within the artiodactyls."
18:38 kcranstn #whalefail
18:38 blackrim so NCBI has it right and those remants in tattered Artiodactyla just need to be marked extinct. shazaam and done
18:38 blackrim word
18:39 blackrim also towodo, how about force_visible for the extinct that we want to be not hidden (but may or may not be in a phylogeny)?
18:40 towodo that can be arranged
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20:03 blackrim towodo, kcranstn: the trees from folks have been uploaded to the google drive. so i am going to do some general checking on these (running them through and checking root mappings) to see if there are taxonomic issues.
20:11 PEM towodo: I've put updated IF files with fossil taxa tagged to the usual place.
20:17 josephwb blackrim: wots the link to the goggle drive new trees?
20:21 blackrim it is in the opentreeoflife final_good_trees folder
20:21 blackrim link here: https://drive.google.com/folderview?id=0B3yKYQFpnM_LbG0tb2QtZFZNNEU&amp;usp=sharing
20:21 blackrim chris mentioned that these were in addition to the ones you have
20:22 blackrim at least the ones in his spread sheet. i think all of yours are in synthesis right? if not, you could just add another sheet and put them there.
20:27 josephwb yeah, chris and i are still finalizing the list.
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20:31 blackrim yeah, feel free to do that. i am doing the plants right now (>800!) so I am sure that in processing those there will be issues either popping up from taxonomy or the studies (already found some)
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